Installation Guide

This guide provides step-by-step instructions to install ACCERT on Windows, macOS, and Linux systems. Please ensure you have administrative privileges on your device, as some steps require it.

Prerequisites

• Git: Ensure Git is installed on your system.

  • Download from Git - Downloads if not already installed.

  • Verify installation by typing git in your terminal; if commands appear, Git is installed.

• Python Coding Environment: While not required, using an IDE like Visual Studio Code is recommended.

• MySQL Community Server: Required for database functionalities.

• NEAMS Workbench: Necessary for integrating ACCERT with the Workbench interface.

Installation Instructions

Choose your operating system to proceed with the installation:

• Installation on Windows

• Installation on macOS

• Installation on Linux

Installation on Windows

For certain aspects of this process, you will need administrative privileges.

Cloning ACCERT

1. Create a Directory for ACCERT:

   • Open your file explorer and create a folder where you want to install ACCERT (e.g., CODE).

2. Open Git Bash or Terminal:

   • Navigate to the directory you just created.

3. Clone the ACCERT Repository:

   $ cd /path/to/CODE
   $ git clone https://github.com/accert-dev/ACCERT.git
   $ cd ACCERT
   

   • Replace /path/to/CODE with the actual path to your CODE directory.

4. Verify Cloning:

   • Ensure the ACCERT folder contains files similar to the ACCERT Git repository.

Install MySQL Community Server

1. Download MySQL:

   • Visit MySQL Community Server and download the recommended version for Windows.

2. Install MySQL:

   • Follow the installation prompts, selecting the Developer Default setup when available.

   Important

   During installation, you will be prompted to create a root password for MySQL. Keep this password secure and accessible; resetting it can be time-consuming and difficult.

   

Install NEAMS Workbench

1. Download NEAMS Workbench:

   • Go to NEAMS Workbench Downloads.

   • Download the .exe file for Windows.

2. Run the Installer:

   • Execute the downloaded file and follow the installation instructions.

   • Note: Your system may flag the installer as unsafe. The file is safe; proceed by selecting the option to keep or run the file.

3. Launch NEAMS Workbench:

   • Open the Workbench application before proceeding to the next steps.

Setting Up ACCERT

1. Navigate to the `src` Directory:

   $ cd src
   

2. Edit the `workbench.sh` File:

   • Open workbench.sh in your Python coding application.

   • Set the workbench_path variable to point to your NEAMS Workbench installation directory. - For example:

    workbench_path="C:/Path/To/Workbench-<version-number>"
   
   - Replace `<version-number>` with the actual version number (e.g., `Workbench-5.3.1`).
   - **Ensure there are no spaces in the folder path**, as this may cause issues.
   

   • Save the file.

3. Run the Setup Script:

   • Open a terminal in the src directory.

   • Execute the setup script:

     $ ./setup_accert.sh
     

   • Note: If you encounter issues running the script, ensure that Git Bash or a Unix-compatible terminal is used.

4. Copy Executables to ACCERT `bin` Directory:

   • Manually create a bin directory inside your ACCERT folder if it doesn’t exist.

   • Navigate to the bin folder inside your NEAMS Workbench installation.

   • Copy sonvalidxml from the Workbench bin folder to the ACCERT/bin folder.

Create and Edit install.conf

1. Create `install.conf`:

   • In the src directory, create a new file named install.conf.

2. Add the Following Content:

   [INSTALL]
   PASSWD = yourpassword
   
   # NOTE: ALL OTHER information should be set up later
   # INSTALL_PATH = /usr/local
   # DATADIR = /mysql/data
   # INSTALL_PACKAGE =
   # EXP_DIR =
   

   • Replace yourpassword with your MySQL root password.

   • Save the file with the exact name install.conf.

   • Ensure file extensions are visible: - In File Explorer, go to View > Show > File name extensions. - Verify that the file is not saved as install.conf.txt.

Install database

1. Navigate to ACCERT/src folder: - type “cmd” in the address bar of the file explorer and press enter.

   $ mysql -h localhost -u root -p
   

   • Enter your MySQL root password when prompted.

   • Run the following command to create the ACCERT database:

   mysql> source accertdb.sql
   

   • Verify that the database has been created by running the following command:

   mysql> show databases;
   

   • You should see accert_db in the list of databases. Then exit the MySQL shell by typing:

   mysql> \q
   

Installation on macOS

For certain aspects of this process, you will need administrative privileges.

Cloning ACCERT

1. Create a Directory for ACCERT:

   • Open your file explorer and create a folder where you want to install ACCERT (e.g., CODE).

2. Open Git Bash or Terminal:

   • Navigate to the directory you just created.

3. Clone the ACCERT Repository:

   $ cd /path/to/CODE
   $ git clone https://github.com/accert-dev/ACCERT.git
   $ cd ACCERT
   

   • Replace /path/to/CODE with the actual path to your CODE directory.

4. Verify Cloning:

   • Ensure the ACCERT folder contains files similar to the ACCERT Git repository.

Install MySQL Community Server

1. Download MySQL:

   • Visit MySQL Community Server and download the recommended version for macOS.

2. Install MySQL:

   • Follow the installation prompts, selecting the Developer Default setup when available.

   • Remember to keep your MySQL root password secure.

Install NEAMS Workbench

1. Download NEAMS Workbench:

   • Go to NEAMS Workbench Downloads.

   • Download the .dmg file for macOS.

2. Run the Installer:

   • Open the downloaded .dmg file and follow the installation instructions.

   • Note: Your system may flag the installer as unsafe. The file is safe; proceed accordingly.

3. Launch NEAMS Workbench:

   • Open the Workbench application before proceeding to the next steps.

Setting Up ACCERT

1. Navigate to the `src` Directory:

   $ cd src
   

2. Edit the `workbench.sh` File:

   • Open workbench.sh in your Python coding application.

   • Set the workbench_path variable to point to your NEAMS Workbench installation directory:

     workbench_path="/Applications/Workbench-<version-number>.app/Contents"
     

     • Replace <version-number> with the actual version number (e.g., Workbench-5.3.1).

   • Save the file.

3. Run the Setup Script:

   • Make the setup script executable:

     $ chmod +x setup_accert.sh
     

   • Execute the setup script:

     $ ./setup_accert.sh
     

Create and Edit install.conf

1. Create `install.conf`:

   • In the src directory, create a new file named install.conf.

2. Add the Following Content:

   [INSTALL]
   PASSWD = yourpassword
   
   # NOTE: ALL OTHER information should be set up later
   # INSTALL_PATH = /usr/local
   # DATADIR = /mysql/data
   # INSTALL_PACKAGE =
   # EXP_DIR =
   

   • Replace yourpassword with your MySQL root password.

   • Save the file with the exact name install.conf.

   • Ensure file extensions are visible: - In File Explorer, go to View > Show > File name extensions. - Verify that the file is not saved as install.conf.txt.

Install database

1. ** connect to MySQL**: .. code-block:: shell

   $ mysql -h localhost -u root -p

   • Enter your MySQL root password when prompted.

   • Run the following command to create the ACCERT database:

   mysql> source accertdb.sql
   

   • Verify that the database has been created by running the following command:

   mysql> show databases;
   

   • You should see accert_db in the list of databases. Then exit the MySQL shell by typing:

   mysql> \q
   

Installation on Linux

For certain aspects of this process, you will need administrative privileges.

Cloning ACCERT

1. Create a Directory for ACCERT:

   • Open your file explorer and create a folder where you want to install ACCERT (e.g., CODE).

2. Open Git Bash or Terminal:

   • Navigate to the directory you just created.

3. Clone the ACCERT Repository:

   $ cd /path/to/CODE
   $ git clone https://github.com/accert-dev/ACCERT.git
   $ cd ACCERT
   

   • Replace /path/to/CODE with the actual path to your CODE directory.

4. Verify Cloning:

   • Ensure the ACCERT folder contains files similar to the ACCERT Git repository.

Install MySQL Community Server

1. Download and Install MySQL:

   • Install MySQL using your distribution’s package manager, or download it from MySQL Community Server.

   # For Debian/Ubuntu
   $ sudo apt-get update
   $ sudo apt-get install mysql-server
   
   # For CentOS/RHEL
   $ sudo yum install mysql-server
   

2. Secure MySQL Installation:

   $ sudo mysql_secure_installation
   

   • Set the root password and follow the prompts.

Install NEAMS Workbench

1. Download NEAMS Workbench:

   • Go to NEAMS Workbench Downloads.

   • Download the .tar.gz file for Linux.

2. Extract and Install:

   $ tar -xzvf Workbench-<version-number>.tar.gz
   $ cd Workbench-<version-number>
   

3. Run the Installer:

   • Follow any additional installation instructions provided.

4. Launch NEAMS Workbench:

   • Run the Workbench application before proceeding to the next steps.

Setting Up ACCERT

1. Navigate to the `src` Directory:

   $ cd src
   

2. Edit the `workbench.sh` File:

   • Open workbench.sh in your Python coding application.

   • Set the workbench_path variable to point to your NEAMS Workbench installation directory:

     workbench_path="/path/to/Workbench-<version-number>"
     

     • Replace <version-number> with the actual version number.

   • Save the file.

3. Run the Setup Script:

   • Make the setup script executable:

     $ chmod +x setup_accert.sh
     

   • Execute the setup script:

     $ ./setup_accert.sh
     

Create and Edit install.conf

1. Create `install.conf`:

   • In the src directory, create a new file named install.conf.

2. Add the Following Content:

   [INSTALL]
   PASSWD = yourpassword
   
   # NOTE: ALL OTHER information should be set up later
   # INSTALL_PATH = /usr/local
   # DATADIR = /mysql/data
   # INSTALL_PACKAGE =
   # EXP_DIR =
   

   • Replace yourpassword with your MySQL root password.

   • Save the file with the exact name install.conf.

Install database

1. ** connect to MySQL**: .. code-block:: shell

   $ mysql -h localhost -u root -p

   • Enter your MySQL root password when prompted.

   • Run the following command to create the ACCERT database:

   mysql> source accertdb.sql
   

   • Verify that the database has been created by running the following command:

   mysql> show databases;
   

   • You should see accert_db in the list of databases. Then exit the MySQL shell by typing:

   mysql> \q
   

Testing the Installation

1. Navigate to the Test Directory:

   $ cd ../test
   

2. Run Tests Using Pytest:

   $ pytest
   

   • This will run the test suite to verify that ACCERT is installed correctly.

Configuration with NEAMS Workbench

1. Open NEAMS Workbench.

2. Add ACCERT Configuration:

   • Go to Workbench > Configurations and click Add.

   • Select Accert from the drop-down menu and click OK.

3. Set Executable Path:

   • In the configuration settings, set the Executable field to the full path of Main.py in the ACCERT/src/ directory.

4. Load Grammar:

   • In the configuration, click Load Grammar to load ACCERT’s input grammar into Workbench.

ACCERT Execution

Through NEAMS Workbench

• Press the Run button within the Workbench interface to execute ACCERT with your selected input file.

Through Command Line

• Execute ACCERT using Python:

  $ python ACCERT/src/Main.py -i myinput.son
  

  • Replace myinput.son with your input file, such as PWR12-BE.son or ABR1000.son.

Troubleshooting

• Conda Errors:

  • Ensure that Conda is correctly installed and accessible in your system’s PATH.

  • Running conda install -r requirements.txt should be done in the environment where ACCERT will run.

  • If you encounter an error like bash: ./conda: Is a directory, ensure you’re referencing the correct path to the Conda executable.

• Workbench Connection Issues:

  • If ACCERT cannot connect to Workbench: - Verify that the workbench_path in workbench.sh is correct and does not contain spaces. - Ensure that you have the necessary permissions to execute scripts.

• Password Issues:

  • If you forget your MySQL root password, refer to MySQL’s official documentation on how to reset the password.

  • It’s crucial to keep your password secure and accessible.

• File Extensions on Windows:

  • Ensure that file extensions are visible: - In File Explorer, go to View > Show > File name extensions.

  • Verify that install.conf is not mistakenly saved as install.conf.txt.

Additional Resources

• ACCERT GitHub Repository: - accert-dev/ACCERT

• NEAMS Workbench Documentation: - NEAMS Workbench User Guide